my first thought is to try plugging the subwoofer into the front outputs of the radio. I dont think this is the issue, but pioneer's have been funny about this in the past.
the only other thing I can think of is that it is a computer hardware/software issue. I know others here have experienced it. I can't tell you if its as simple as turning the bass up within your sound card control panel, but you can try it.
does the subwoofer still work, just at a lower level?